This study is focused on the optimization and decreasing the metal ion content in jatropha biodiesel using an ion exchange resin. The changes in the organic composition of jatropha oil biodiesel were measured by GCMS before and after passing the biodiesel over the ion exchange resin. The chelating efficiency of ion exchange resin on metal ions, including potassium, calcium, sodium, and magnesium, in jatropha biodiesel either treated with different oleic acid content or having different oxidation degrees was evaluated. The results showed that the ion exchange resin can effectively decrease the metal ions content in jatropha biodiesel without producing harmful substances to environment and human body. Moreover, the increase in oleic acid content and oxidation in Jatropha biodiesel affects the ability of ion exchange resins to sequester metal ions.